Abstract:
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Recent advances in high-throughput technology permit genome-wide gene expression measurement at the single cell level. Single-cell RNA-Sequencing (scRNA-Seq) is the most widely and has been used in numerous publications. Although systematic errors, including batch effects, have been widely reported as a major challenge in high-throughput technologies, these issues have received minimal attention in published studies based on scRNA-Seq technology. Here, we examine data from published studies and found that systematic errors can explain a substantial percentage of observed cell-to-cell expression variability. Specifically, we show that scRNA-Seq reports more zeros than expected, and that technical variability can lead to cell-to-cell differences that can be confused with novel biological results. Finally, we demonstrate how batch-effects can exacerbate the problem.
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